CreatePredAlphaCost pred_alpha2k alpha11 T0216.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0216.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 1

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file
#	maybe_ssbond 0.5

// For comparative modeling, increase weight of break and hbond_geom...

// put any constraints here, such as helix constraints, strand constraints,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

# include T0216.t2k.dssp-ehl2.constraints
# include T0216.t2k.dssp-ebghstl.constraints
# include T0216.t2k.stride-ebghtl.constraints
# include T0216.t2k.str2.constraints
# include T0216.t2k.alpha.constraints
# include T0216.t2k.bys.constraints

# for try2, I'm going with the t2k constraints
# switching back to t04 for hairpins in try7
# EXCEPT for some 'bogus' helices
HelixConstraint 	F3	K16	2.613
StrandConstraint	E20	L26	0.6364
StrandConstraint	F31	R34	0.603
StrandConstraint	N50	K57	0.6225
StrandConstraint	F64	Q67	0.6023
HelixConstraint 	E73	S81	2.6412
HelixConstraint 	K117	A130	2.6182
StrandConstraint	V136	M138	0.761
# HelixConstraint 	K145	T154	0.6474
# HelixConstraint 	F171	A176	0.6017
HelixConstraint 	P198	L212	2.6601

# include T0216.t04.dssp-ehl2.constraints
# include T0216.t04.dssp-ebghstl.constraints
# include T0216.t04.stride-ebghtl.constraints
# include T0216.t04.str2.constraints

include T0216.t04.alpha.constraints
include T0216.t04.bys.constraints

# let's try an make a couple of hairpins
# Constraint L35.CB L40.CB	0 5 9	5.0
# Constraint K57.CB T61.CB	0 5 9	5.0

# for try3, we add some sheets (hope we have directions right)
# for try4, I changed the next one's hbond
# for try5, we 'break' the sheets but bind the ends
SheetConstraint	V51 V55 	F64 K60 	10.0 # hbond K54
# Constraint K57.CB K60.CB -10 7.0 12.0 5.0
# Constraint I53.CB F64.CB -10 7.0 12.0 5.0
# SheetConstraint A36 S32 	D39 Y43 	hbond A36	7.0
# Constraint A36.CB D39.CB -10 7.0 12.0 5.0
# Constraint S32.CB Y43.CB -10 7.0 12.0 5.0
# for try4, I'm adding this next one.
# SheetConstraint E27 I23 	F31 L35 	10.0 # hbond E27	10.0
# Constraint E27.CB F31.CB -10 7.0 12.0 5.0
# Constraint I23.CB L35.CB -10 7.0 12.0 5.0

# for try6 we examine 21-35 ^v 
# for try6 we'll add this connection
SheetConstraint V21 A36 	K54 D39 	10.0
StrandConstraint V21 A36	10.0
StrandConstraint D39 K54	10.0

# for try2, I'm including the first 2 rr constraints
# and some with bonuses
Constraint S24.CB K151.CB -10. 7.0 12.0 0.633
Constraint S24.CB N50.CB -10. 7.0 12.0 0.608
Constraint S24.CB K54.CB -10. 7.0 12.0 0.522	bonus
Constraint S24.CB T61.CB -10. 7.0 12.0 0.514	bonus
Constraint Q22.CB K54.CB -10. 7.0 12.0 0.489	bonus
Constraint S24.CB S163.CB -10. 7.0 12.0 0.486	bonus
Constraint S24.CB T63.CB -10. 7.0 12.0 0.466	bonus
Constraint Q22.CB E52.CB -10. 7.0 12.0 0.445	bonus